Polymorphisms in the Kappa-Casein Gene Across Diverse Cattle Breeds: In silico Characterization, Genetic Variant and their Implications for Dairy Production

This study investigated polymorphism and evolutionary relationships at the CSN3 locus across selected cattle breeds and related bovine taxa using a comparative in silico approach. Publicly available GenBank sequences representing Bos taurus alleles and pseudogene-like sequences, Bos indicus , Bos gaurus , Bos javanicus , Bison bison , a Bos taurus × Bos indicus hybrid, and Bubalus species were analysed to assess sequence variation, nucleotide composition, codon usage, genetic diversity, and phylogenetic relationships. Sequence alignment and pairwise comparisons indicated substantial conservation across the genus Bos , alongside notable variation among B. taurus sequences. Among the functional allelic forms examined, the A and B alleles exhibited comparatively greater sequence divergence, whereas the E allele showed high sequence similarity to the A allele. The sequences designated AA and BB displayed marked divergence from the functional allelic forms, although their non-functional status requires confirmation through additional evidence. Phylogenetic analysis revealed close relationships among the sampled Bos taxa, while Bubalus formed a more distinct lineage, consistent with broader evolutionary relationships among bovine taxa. Nucleotide diversity and the distribution of segregating sites further indicated substantial sequence variation within the sampled B. taurus sequences. These findings suggest that the CSN3 locus is relatively conserved across the examined taxa but exhibits sufficient variation within B. taurus to warrant further investigation as a candidate marker for dairy cattle characterisation and breeding. The study provides a comparative sequence-based framework for investigating CSN3 diversity and its potential associations with milk composition and processing properties. However, the practical utility of the identified variants for breeding decisions requires validation using phenotype-linked datasets and larger, representative cattle populations.